1ZV2

Cu-containing nitrite reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of the oxidized and reduced forms of nitrite reductase from Rhodobacter sphaeroides 2.4.3 at high pH: changes in the interactions of the type 2 copper.

Jacobson, F.Guo, H.Olesen, K.Okvist, M.Neutze, R.Sjolin, L.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1190-1198

  • DOI: https://doi.org/10.1107/S0907444905017488
  • Primary Citation of Related Structures:  
    1ZV2, 2A3T

  • PubMed Abstract: 

    Nitrite reductase is an enzyme operating in the denitrification pathway which catalyses the conversion of nitrite (NO2(-)) to gaseous nitric oxide (NO). Here, crystal structures of the oxidized and reduced forms of the copper-containing nitrite reductase from Rhodobacter sphaeroides 2.4.3 are presented at 1.74 and 1.85 A resolution, respectively. Whereas the structure of the enzyme is very similar to those of other copper-containing nitrite reductases, folding as a trimer and containing two copper sites per monomer, the structures reported here enable conformational differences between the oxidized and reduced forms of the enzyme to be identified. In the type 1 copper site, a rotational perturbation of the side chain of the copper ligand Met182 occurs upon reduction. At the type 2 copper site, a dual conformation of the catalytic residue His287 is observed in the oxidized structure but is lacking in the reduced structure, such that the interactions of the oxidized type 2 copper ion can be regarded as adopting octahedral geometry. These findings shed light on the structural mechanism of the reduction of a copper-bound nitrite to nitric oxide and water.


  • Organizational Affiliation

    Department of Chemistry and Bioscience, Chalmers University, Box 462, SE-405 30 Göteborg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-containing nitrite reductase328Cereibacter sphaeroidesMutation(s): 0 
Gene Names: nirK
EC: 1.7.2.1
UniProt
Find proteins for Q53239 (Cereibacter sphaeroides (strain ATCC 17025 / ATH 2.4.3))
Explore Q53239 
Go to UniProtKB:  Q53239
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53239
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.381α = 90
b = 72.381β = 90
c = 147.509γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description